siggenes

DOI: 10.18129/B9.bioc.siggenes  

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Bioconductor version: Release (3.16)

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Author: Holger Schwender

Maintainer: Holger Schwender <holger.schw at gmx.de>

Citation (from within R, enter citation("siggenes")):

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("siggenes")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("siggenes")

 

HTML identify.sam.html
HTML plot.ebam.html
HTML plot.finda0.html
HTML plot.sam.html
HTML print.ebam.html
HTML print.finda0.html
HTML print.sam.html
PDF R Script siggenes Manual
PDF siggenesRnews.pdf
HTML summary.ebam.html
HTML summary.sam.html
PDF   Reference Manual

Details

biocViews DifferentialExpression, ExonArray, GeneExpression, Microarray, MultipleComparison, SNP, Software
Version 1.72.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License LGPL (>= 2)
Depends Biobase, multtest, splines, methods
Imports stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
LinkingTo
Suggests affy, annotate, genefilter, KernSmooth
SystemRequirements
Enhances
URL
Depends On Me KCsmart
Imports Me coexnet, DeSousa2013, minfi, trio, XDE
Suggests Me GCSscore, logicFS
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package siggenes_1.72.0.tar.gz
Windows Binary siggenes_1.72.0.zip
macOS Binary (x86_64) siggenes_1.72.0.tgz
macOS Binary (arm64) siggenes_1.72.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/siggenes
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/siggenes
Bioc Package Browser https://code.bioconductor.org/browse/siggenes/
Package Short Url https://bioconductor.org/packages/siggenes/
Package Downloads Report Download Stats

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